[gmx-users] relative binding free energy calculation Gromacs 5.0.5

[Stefania Evoli]

Dear users,

I’m performing relative binding free energy calculation in Gromacs 5.0.5. In the mdp files I’m using the following section


free-energy              = yes

init_lambda_state        = LAMBDA

fep_lambdas              = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0  1.0 1.0  1.0 1.0  1.0 1.0  1.0

vdw_lambdas              = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0

;couple-moltype           = LIG

;couple-lambda0           = vdw-q

;couple-lambda1           = none

;couple-intramol          = no

sc-alpha                 = 0.5

sc-sigma                 = 0.3

sc-power                 = 1.0

sc-r-power               = 6

sc-coul                  = no

nstdhdl                  = 100

calc-lambda-neighbors    = -1


And I obtained the following values


 0 -- 1        16.498  +-  0.147     16.458  +-  0.173     18.142  +-  0.465     13.644  +-  0.351     16.264  +-  0.411     16.264  +-  0.413

   1 -- 2         7.086  +-  0.143      6.982  +-  0.159     10.223  +-  0.246      4.168  +-  0.299      6.971  +-  0.341      6.971  +-  0.454

   2 -- 3        -1.954  +-  0.114     -1.685  +-  0.129     -1.043  +-  0.574     -3.884  +-  0.392     -1.883  +-  0.356     -1.883  +-  0.356

   3 -- 4       -13.604  +-  0.139    -13.271  +-  0.145    -10.960  +-  0.574    -18.048  +-  0.234    -14.286  +-  0.601    -13.222  +-  0.167

   4 -- 5         0.089  +-  0.003      0.093  +-  0.003      0.079  +-  0.005      0.099  +-  0.003      0.091  +-  0.003      0.085  +-  0.000

   5 -- 6         0.078  +-  0.004      0.079  +-  0.004      0.094  +-  0.003      0.062  +-  0.008      0.087  +-  0.003      0.080  +-  0.000

   6 -- 7         0.141  +-  0.008      0.130  +-  0.011      0.110  +-  0.017      0.170  +-  0.001      0.170  +-  0.001      0.143  +-  0.001

   7 -- 8         0.123  +-  0.005      0.131  +-  0.006      0.155  +-  0.001      0.096  +-  0.011      0.154  +-  0.001      0.121  +-  0.001

   8 -- 9         0.063  +-  0.005      0.063  +-  0.006      0.071  +-  0.011      0.056  +-  0.001      0.056  +-  0.001      0.095  +-  0.001

   9 -- 10        0.012  +-  0.004      0.002  +-  0.005      0.028  +-  0.001     -0.004  +-  0.008      0.028  +-  0.001      0.065  +-  0.001

  10 -- 11        0.019  +-  0.008      0.030  +-  0.011     -0.036  +-  0.009      0.084  +-  0.011      0.007  +-  0.007      0.027  +-  0.001

  11 -- 12        0.016  +-  0.006      0.013  +-  0.007      0.019  +-  0.008      0.008  +-  0.009      0.018  +-  0.006     -0.004  +-  0.000

  12 -- 13        0.012  +-  0.007      0.015  +-  0.008     -0.004  +-  0.010      0.028  +-  0.009      0.012  +-  0.007     -0.018  +-  0.000

  13 -- 14       -0.011  +-  0.008     -0.010  +-  0.009      0.015  +-  0.011     -0.034  +-  0.010     -0.011  +-  0.008     -0.034  +-  0.000

  14 -- 15       -0.049  +-  0.006     -0.049  +-  0.007     -0.055  +-  0.014     -0.044  +-  0.001     -0.044  +-  0.001     -0.054  +-  0.000

  15 -- 16       -0.085  +-  0.003     -0.086  +-  0.004     -0.065  +-  0.001     -0.104  +-  0.005     -0.066  +-  0.001     -0.078  +-  0.001

  16 -- 17       -0.116  +-  0.009     -0.116  +-  0.010     -0.132  +-  0.006     -0.100  +-  0.016     -0.129  +-  0.006     -0.109  +-  0.001

  17 -- 18       -0.150  +-  0.009     -0.145  +-  0.010     -0.129  +-  0.018     -0.159  +-  0.001     -0.159  +-  0.001     -0.151  +-  0.001

  18 -- 19       -0.218  +-  0.005     -0.220  +-  0.005     -0.219  +-  0.002     -0.218  +-  0.008     -0.219  +-  0.002     -0.211  +-  0.001

It is clear the instability of the first four lambda values. Can someone suggest me a way to avoid it? I’m trying to use different sc-alpha, sc-power and sc-r-power. Any suggestion?

Thank you,
Stefania

—
Dr. Stefania Evoli
Post-Doctoral Fellow
King Abdullah University of Science and Technology
Catalysis center - Bldg. 3, 4th floor, 4231–WS18
Thuwal, Kingdom of Saudi Arabia
stefania.evoli at kaust.edu.sa



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